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Beacon Development

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Talk on Beacon Development at the Global Alliance for Genomics and Health Plenary Meeting 2016, Vancouver, BC, Canada.

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Beacon Development

  1. 1. genomicsandhealth.org Beacon Development 17/10/2016 Miro Cupak
  2. 2. https://github.com/ga4gh/beacon-team2 What is this about? Beacon API specification: https://github.com/ga4gh/beacon-team What else is out there?
  3. 3. https://github.com/ga4gh/beacon-team3 Beacon Development Kits (BDK) • Open-source quickstarts. • Compliant with the latest beacon specification. • Proven to work well. • Available in: • Java • https://github.com/mcupak/beacon-java • Python • https://github.com/mcupak/beacon-python • JavaScript • https://github.com/mcupak/beacon-javascript
  4. 4. https://github.com/ga4gh/beacon-team4 Java BDK • Most advanced of the BDKs. • Effectively a reference implementation. • Provides: • Compatible beacon API. • Sample beacon implementation. • Integration of Beacon data models. • Various utilities: output serialization, input normalization, error handling and status code mapping… • Test suite. • Security (prototype).
  5. 5. https://github.com/ga4gh/beacon-team5 BDK adapter system • Adapter API: • https://github.com/mcupak/beacon-adapter-api • Adapter implementations for common data stores/APIs: • https://github.com/mcupak/beacon-adapters • 3 adapters OOTB: • Variants API • variant set beacon dataset • Annotation API • annotation set beacon dataset • VCF • file beacon dataset • Easy to implement your own and plug into Java BDK.
  6. 6. https://github.com/ga4gh/beacon-team6 Beaconizer • Extension of Java BDK for more complex beaconizing. • Support for multiple adapters and multiple beacons. • Open-source: https://github.com/mcupak/beaconizer GET /beacons GET /beacons/:id GET /beacons/:id/query
  7. 7. https://github.com/ga4gh/beacon-team7 Beacon implementations • Java • https://github.com/elixirhub/human-data-beacon • https://github.com/prota/cnag-beacon • Python • https://github.com/Genecloud/simplebeacon • https://github.com/maximilianh/ucscBeacon • https://github.com/kozbo/Beacon-on-GA4GH-API • JavaScript • https://github.com/ElementoLab/beacon • Go • https://github.com/googlegenomics/beacon-go
  8. 8. https://github.com/ga4gh/beacon-team8 Client library • Query beacons from Java. • Integration with Beacon 0.3 schema. • Open-source: https://github.com/mcupak/beacon-client
  9. 9. https://github.com/ga4gh/beacon-team9 CLI • Query beacons from your shell. • Open-source: https://github.com/mcupak/beacon-cli $ java -jar beacon-cli.jar -u http://localhost:5000/test/ response —help Description: Gets response to a beacon query for allele information. Usage: -a (--assembly-id) VAL : Assembly ID (GRC notation, e.g. 'GRCh37'). -ab (--alternate-bases) VAL : The bases that appear instead of the reference bases. Accepted values: see the ALT field in VCF 4.2 specification (https://samtools.github.io/hts-specs/VCFv4. 2.pdf). … $ java -jar beacon-cli.jar -u http://localhost:5000/test/ response -a GRCh37 -ab A -r 1 -rb T -s 1000 { "beaconId": "test", "exists": true, "alleleRequest": … }
  10. 10. https://github.com/ga4gh/beacon-team10 Compliance suite • Test beacon compatibility with 0.3 specification. • Groovy-based prototype. • Open source: https://github.com/mcupak/beacon-compliance
  11. 11. https://github.com/ga4gh/beacon-team11 Other utilities • Coordinate conversion library. • Wraps Liftover and HGVS. • Extensible, with built-in converters for standard assemblies. • Open-source: https://github.com/mcupak/genome-coordinates- converter
  12. 12. https://github.com/ga4gh/beacon-team12 Questions? miro@dnastack.com https://git.io/vPifs Any tools we’re missing? Huge thanks to the Beacon team and our summer students Patrick and Artem.

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